MolNFT v1 · #186257 · protein
Crystal structure of HLA-B*5301 complex with an HIV-1 gag-derived epitope QW9
7R7V · MHC class I antigen: “Crystal structure of HLA-B*5301 complex with an HIV-1 gag-derived epitope QW9”. X-ray diffraction, 4 pockets (best druggability 0.68). MolNFT v1 #186257 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7R7V
- Type
- protein
- Length
- 385 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Gln-ala-ser-gln-glu-val-lys-asn-TRP
- UniProt
- S6BVK3, P61769
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 276 | 26% helix, 39% strand | S6BVK3 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Gln-ala-ser-gln-glu-val-lys-asn-TRP | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.68 | 0.77 | 53 | empty |
| 2 | 128 | 0.49 | 0.79 | 23 | empty |
| 3 | 96 | 0.42 | 0.78 | 21 | GOL |
| 4 | 70 | 0.38 | 0.78 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1398 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 932 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7R7V · Crystal structure of HLA-B*5301 complex with an HIV-1 Gag-derived epitope QW9 · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt S6BVK3
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 7R7V · PDBe 7R7V · UniProt S6BVK3 · UniProt P61769
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